SUMMARY: Access pathways in enzymes are crucial for the passage of substrates and products of catalysed reactions. The process can be studied by computational means with variable degrees of precision. Our in-house approximative method CaverDock provides a fast and easy way to set up and run ligand binding and unbinding calculations through protein tunnels and channels. Here we introduce pyCaverDock, a Python3 API designed to improve user experience with the tool and further facilitate the ligand transport analyses. The API enables users to simplify the steps needed to use CaverDock, from automatizing setup processes to designing screening pipelines. AVAILABILITY AND IMPLEMENTATION: pyCaverDock API is implemented in Python 3 and is freely available with detailed documentation and practical examples at https://loschmidt.chemi.muni.cz/caverdock/.

MP net is a formal model specifically designed for the field of parallel applications that use message passing interface. The main idea is to use MP net as a comprehensible way of presenting the actual structure of communication within MPI applications. The goal is to provide users with the kind of feedback that can help them to check quickly whether or not the actual communication within their application corresponds to the intended one. This paper introduces MP net that focuses on the communication part of parallel applications and emphasizes its spatial character, which is rather hidden in sequential (textual) form.

Parallel computing can be very useful for meta-heuristic algorithms, because it can reduce time to find a solution with given properties. On the other hand parallel programming is generally more difficult than the sequential one and we need more development time to get a working parallel solution. We are developing a tool named Kaira which is intended for modelling, debugging, and automated generation of parallel applications. The modelling is based on our own variant of Coloured Petri Nets. In this paper we present how to create parallel programs from an existing sequential implementation of Ant Colony Optimization Algorithm using Kaira. This approach simplifies the development process and thus saves the development time and costs.

The paper describes how to use the image specific segments in search. Particularly it refers to the coins photos, which means we need to regard rotations and different deformations of the images. Possibilities of the images preprocessing are briefly described in the introduction. A great number of images which seems the same at first glance, but differs in details, they may have different texts, symbols, etc. The article deals with proper algorithms for selection of such specific segments, processing, saving and application in search.